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lammps/examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.g++.8
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LAMMPS (1 Feb 2014)
# SRD diffusion demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
4 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
Memory usage per processor = 3.31932 Mbytes
Step Temp rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051714 2.5292571 1.1630889
800 2.7632971 2.9060854 -0.52075339 2.2149107 0.77106814
900 2.9905601 2.8869672 -0.49099457 2.4696599 0.69616725
1000 2.8470146 2.9004954 -0.51281252 2.305732 0.68820531
Loop time of 0.0485955 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.0201517 (41.4682)
Neigh time (%) = 0.000492364 (1.01319)
Comm time (%) = 0.0191883 (39.4858)
Outpt time (%) = 0.000273198 (0.562188)
Other time (%) = 0.00848994 (17.4706)
Nlocal: 12.5 ave 16 max 8 min
Histogram: 1 1 0 0 0 3 0 0 1 2
Nghost: 34.125 ave 42 max 28 min
Histogram: 1 0 2 2 0 1 0 1 0 1
Neighs: 46.125 ave 65 max 20 min
Histogram: 1 0 1 0 1 2 0 0 1 2
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
create_atoms 2 region plane
Created 85849 atoms
set type 2 mass 0.01
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z # quatw quati quatj quatk
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
SRD per actual grid cell = 1.92757
SRD viscosity = 0.688101
big/SRD mass density ratio = 1.37367
# of rescaled SRD velocities = 0
ave/max small velocity = 13.3093 24.3359
ave/max big velocity = 2.08028 5.05671
Memory usage per processor = 10.9077 Mbytes
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 2.9004954 2.9004954 0 0.025582146 -0.51281252 3.8089257 0.89865242 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.3106106 3.3106106 1.0635866 0.029956176 -0.47263474 4.4601751 1.8111247 14000 35 160 0 224946 98040 11449 4182 1.0635866 1047 50 0
2000 2.2814487 2.2814487 1.2237286 0.017972589 -0.72341981 2.6759388 1.3454977 15318 47 276 0 528340 98040 11449 4136 1.2237286 2383 50 0
3000 4.2476485 4.2476485 1.2992612 0.038526442 -0.59279435 5.7362019 1.6896403 16506 63 410 0 830594 98040 11449 4172 1.2992612 3834 50 0
4000 2.4798681 2.4798681 1.3453264 0.022837826 -0.29467953 3.4003239 2.0765724 17201 51 403 0 1185573 98040 11449 4233 1.3453264 5456 50 0
5000 3.0852629 3.0852629 1.3915904 0.02760985 -0.48621111 4.1108305 1.2676357 17540 61 591 0 1594856 98040 11449 4306 1.3915904 7419 50 0
6000 6.7201122 6.7201122 1.3649223 0.064627842 -0.39052776 9.6224394 2.5524159 17997 59 564 0 2010250 98040 11449 4213 1.3649223 9280 50 0
7000 2.720343 2.720343 1.3909677 0.024282471 -0.43789405 3.6154171 1.5288376 17922 64 342 0 2392388 98040 11449 4228 1.3909677 10947 50 0
8000 1.9181626 1.9181626 1.3514483 0.014305579 -0.72810462 2.1299577 0.89423917 18188 42 260 0 2751626 98040 11449 4236 1.3514483 12556 50 0
9000 2.9090186 2.9090186 1.3688847 0.02558926 -0.52445278 3.8099849 1.1756318 18536 63 440 0 3112508 98040 11449 4227 1.3688847 14164 50 0
10000 1.9647403 1.9647403 1.3979066 0.015375037 -0.63827389 2.2891892 0.65597214 18817 60 466 0 3501352 98040 11449 4257 1.3979066 16016 50 0
11000 1.9989051 1.9989051 1.3872043 0.016191243 -0.56765443 2.4107142 0.80582429 18756 58 767 0 3856028 98040 11449 4254 1.3872043 17611 50 0
12000 1.7538755 1.7538755 1.4594883 0.013930543 -0.53915598 2.0741185 1.0563875 18602 58 335 0 4248666 98040 11449 4251 1.4594883 19350 50 0
13000 13.730871 13.730871 1.4864545 0.13447802 -0.43656501 20.022433 3.6701166 19144 74 681 0 4708523 98040 11449 4104 1.4864545 21589 50 0
14000 5.1078782 5.1078782 1.3637807 0.049721182 -0.20775172 7.4029868 2.559935 18494 65 713 0 5139143 98040 11449 4167 1.3637807 23555 50 0
15000 2.5843962 2.5843962 1.3450247 0.022294373 -0.53134114 3.3194092 1.1069147 18489 52 260 0 5489252 98040 11449 4262 1.3450247 25209 50 0
ERROR: Lost atoms: original 14889 current 14819 (../thermo.cpp:392)
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